AmbiDose: per-cell removal budgets for ambient RNA contamination

Abstract

Ambient RNA contamination confounds expression analysis in droplet-based single-cell and single-nucleus RNA sequencing. Here we present AmbiDose, which combines an ambient profile estimated from empty droplets with cell-specific nominal removal budgets and expression-based protection of lineage-enriched genes. Its ambient dose guides count removal rather than estimating a calibrated contamination fraction. In a held-out human-mouse GEM-X mixture, AmbiDose removed 92.0% of cross-species UMIs while retaining 99.6% of same-species UMIs. It reduced off-target marker expression in kidney-tumor and fetal-liver cohorts and yielded the lowest proximal-tubule marker leakage among the tested methods across five strain-mixed kidney libraries. Simulations supported the contribution of cell-specific dose estimates but identified reduced endogenous retention or incomplete removal when ambient and endogenous expression overlapped. AmbiDose is available as a Python package compatible with Scanpy.

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Cite

BibTeX RIS

BibTeX

@misc{li2026ambidose,
  title = {{AmbiDose: per-cell removal budgets for ambient RNA contamination}},
  author = {Z. Li and A. W. James and S. Li},
  howpublished = {bioRxiv},
  year = {2026},
  month = sep,
  doi = {10.64898/2026.09.27.754849},
  url = {https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1},
  note = {CC BY},
}

RIS

TY  - UNPB
TI  - AmbiDose: per-cell removal budgets for ambient RNA contamination
AU  - Z. Li
AU  - A. W. James
AU  - S. Li
PY  - 2026
DA  - 2026/09/27
PB  - bioRxiv
DO  - 10.64898/2026.09.27.754849
UR  - https://www.biorxiv.org/content/10.64898/2026.09.27.754849v1
AB  - Ambient RNA contamination confounds expression analysis in droplet-based single-cell and single-nucleus RNA sequencing. Here we present AmbiDose, which combines an ambient profile estimated from empty droplets with cell-specific nominal removal budgets and expression-based protection of lineage-enriched genes. Its ambient dose guides count removal rather than estimating a calibrated contamination fraction. In a held-out human-mouse GEM-X mixture, AmbiDose removed 92.0% of cross-species UMIs while retaining 99.6% of same-species UMIs. It reduced off-target marker expression in kidney-tumor and fetal-liver cohorts and yielded the lowest proximal-tubule marker leakage among the tested methods across five strain-mixed kidney libraries. Simulations supported the contribution of cell-specific dose estimates but identified reduced endogenous retention or incomplete removal when ambient and endogenous expression overlapped. AmbiDose is available as a Python package compatible with Scanpy.
ER  -

Abstract

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